Large-Scale Computational Modeling of H5 Influenza Variants Against HA1-Neutralizing Antibodies

Colby T. Ford, Shirish Yasa, Khaled Obeid, Rafael Jaimes III, Phillip J. Tomezsko,
Sayal Guirales-Medrano, Richard Allen White III, and Daniel Janies

Media Mentions

• "The Great Cellular Heist" - Inside UNC Charlotte: https://inside.charlotte.edu/featured-stories/the-great-cellular-heist/
• US News: https://www.usnews.com/news/health-news/articles/2025-04-05/experts-warn-bird-flu-could-pose-growing-risk-to-human-health
• Forbes: https://www.forbes.com/sites/innovationrx/2025/04/02/innovationrx-trump-administration-health-agency-layoffs-threaten-biotech-innovation/
• Eureka Alert: https://www.eurekalert.org/news-releases/1077418

Data

Outputs:

• Docking metrics, antigen/antibody metadata, and clustering results: Experiments.xlsx
• Docked structures ($n=1,804$): data/results
• Phylogenetic Tree: tree0.tnt.nex

Inputs:

• Antigens ($n=164$):
  • Input Sequences: data/sequences
  • Predicted Structures: data/structures/antigens/HA1
• Antibodies ($n=11$):
  • Structures: data/structures/antibodies

Workflow

Scripts

0. Sequence Collection: 0_sequence_collection
1. Structure Generation with ColabFold: 1_structure_generation
2. PDB Structure Preparation: 2_structure_prep
3. HADDOCK3 Experiment Generation: 3_experiment_generation
4. HPC Experiment Submission: 4_experiment_submission
5. Cleanup: 5_cleanup
6. Metrics Collection: 6_metrics_collection
7. Analyses: 7_analyses
   • Statistics: 7_analyses/statistics
   • Structure Analyses: 7_analyses/statistics
   • Phylogenetics: 7_analyses/phylogenetics
   • GIRAF Graph Analyses: scripts/7_analyses/giraf

Citation

Ford, C. T., Yasa, S., Obeid, K., Jaimes III, R., Tomezsko, P. J., Guirales-Medrano, S., White III, R. A., and Janies, D. (2025). Large-scale computational modelling of H5 influenza variants against HA1-neutralising antibodies. eBioMedicine, 114. doi:10.1016/j.ebiom.2025.105632

@article{ford2025,
    author = {Ford, Colby T. and Yasa, Shirish and Obeid, Khaled and Jaimes III, Rafael and Tomezsko, Phillip J. and Guirales-Medrano, Sayal and White III, Richard Allen and Janies, Daniel},
    title = {{Large-Scale Computational Modelling of H5 Influenza Variants Against HA1-Neutralising Antibodies}},
    year = {2025},
    month = {Apr},
    day = {01},
    publisher = {Elsevier},
    volume = {114},
    issn = {2352-3964},
    doi = {10.1016/j.ebiom.2025.105632},
    url = {https://doi.org/10.1016/j.ebiom.2025.105632},
    journal = {Lancet eBioMedicine}
}